MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2r8s:R1004, See in JSmolClick on the image to toggle views Site type: 2Ob Schematic drawing for 2Ob List of all 1662 Mg2+ binding sites with the site type 2Ob in RNA crystal structures in the full dataset (switch to benchmark dataset) Sites in the table can be ordered by the following fields by clicking the column header: "benchmark dataset", "Coordination Number", "Qv #", "Qs #", "Qe #", "PDB ID" or "Mg2+ ID" Page 16 of 67 | « Previous | Next » | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4qcr A3628 2Ob 3   0.17   0.37   0.96 no 4dr3 A1717 2Ob 3   0.20   0.17   0.89 no 4qcp A3316 2Ob 3   0.17   0.31   0.89 no 3d5d A3456 2Ob 2   0.05   0.29   0.37 no 4b3m A2749 2Ob 2   0.12   0.17   0.87 no 3v29 B202 2Ob 2   0.03   0.17   0.94 no 3u5d 13948 2Ob 2   0.03   0.14   0.78 no 1vw0 A3209 2Ob 2   0.04   0.24   0.61 no 4b3t A2657 2Ob 2   0.04   0.21   0.91 no 4l6j A5190 2Ob 2   0.02   0.13   0.70 no 4kx2 A3210 2Ob 2   0.08   0.22   0.87 no 3f1f A5597 2Ob 2   0.03   0.18   0.82 no 1vvq A3205 2Ob 2   0.08   0.30   0.86 no 3ohz A3018 2Ob 2   0.03   0.22   0.82 no 4gas A1669 2Ob 2   0.04   0.19   0.86 no 4qd1 A3212 2Ob 2   0.07   0.22   0.79 no 3d5b A3406 2Ob 2   0.03   0.18   0.19 no 4l6j A5081 2Ob 2   0.04   0.18   0.75 no 1vxl A3204 2Ob 2   0.09   0.31   0.95 no 3knl A1640 2Ob 2   0.09   0.19   0.67 no 3kiw A3093 2Ob 2   0.04   0.26   0.68 no 3i8h A1910 2Ob 2   0.07   0.16   0.95 no 1vy1 A3196 2Ob 2   0.08   0.22   0.76 no 3kiy A3006 2Ob 2   0.04   0.17   0.61 no 4qcr A3066 2Ob 2   0.06   0.17   0.98 no

^# Validation parameters Q_v, Q_s, Q_e are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Q_v measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg²⁺ (+2)
Q_s measures the geometrical symmetry of the ligands distribution around the Mg²⁺ required for octahedral geometry
Q_e measures the agreement of the isotropic atomic displacement (B) factor and occupancy of the Mg²⁺ compared to those of all atoms in its environment

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout nucleobase moiety
Reference:	Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

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